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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit d93e1dd276027cfc3fb518236110395a23d96f66
author thomaswollmann
date Wed, 16 Jan 2019 15:29:41 -0500
parents 626be11c43fc
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babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
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1 <tool id="anisotropic_diffusion" name="Anisotropic Diffusion" version="0.1">
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2 <description>Edge-preserving, Anisotropic diffusion</description>
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3 <requirements>
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4 <requirement type="package" version="0.14.0" >scikit-image</requirement>
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5 <requirement type="package" version="0.3.0">medpy</requirement>
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6 <requirement type="package" version="1.15.4">numpy</requirement>
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babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
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7 </requirements>
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8 <command>
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9 <![CDATA[
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10 python "$__tool_directory__/anisotropic_diffusion.py" '$input' '$output' '$niter' '$kappa' '$gamma' '$eqoption'
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param name="input" type="data" format="tiff" label="Image file"/>
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babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
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15 <param label="Number of iterations" name="niter" optional="true" type="integer" value="50"/>
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
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16 <param label="Conduction coefficient" name="kappa" optional="true" type="integer" value="50"/>
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
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17 <param label="Speed of diffusion" name="gamma" optional="true" type="float" value="0.1"/>
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18 <param name="eqoption" type="select" label="Diffusion Feature" help="Perona Malik diffusion equation">
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19 <option value="1" selected="True">Favour high contrast edges</option>
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20 <option value="2">Favour wide regions</option>
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21 </param>
babb41158e9f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/anisotropic-diffusion/ commit 3036169a656a17a8c73a93241e375693f281bce8
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22 </inputs>
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23 <outputs>
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24 <data format="tiff" name="output"/>
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25 </outputs>
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26 <tests>
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27 <test>
1
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28 <param name="input" value="galaxyIcon_noText.tif" />
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29 <param name="niter" value="100" />
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30 <param name="kappa" value="50" />
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31 <param name="gamma" value="0.1" />
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32 <param name="eqoption" value="1" />
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33 <output name="output" file="res.tif" ftype="tiff" compare="sim_size"/>
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34 </test>
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35 </tests>
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36 <help>Edge-preserving, Anisotropic image diffusion.</help>
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37 <citations>
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38 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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39 </citations>
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40 </tool>